Abstract The objectives of Specific Aim #3 will be to continue with genotyping for STRs and MHC class I alleles, and facilitate the transition to the SNP panel developed by the Genetics and Genomics Working Group (GGWG) of the NPCR Consortium. An STR panel that was designed for genetic management will be used for parentage assessment and estimating the population genetic metrics of the SPF animals. Genotyping based on this panel of STRs will be conducted at the Veterinary Genetics Laboratory (VGL) where these analyses are already being performed on a routine basis. The genetic information from this panel of markers will be used to develop multigenerational pedigrees and also maintain the SPF colony genetic diversity. Determination of MHC Class I types will also be performed at the VGL based on a panel of MHC-linked STRs. This, in combination with segregation analysis in animals with known pedigrees, will allow the establishment zygosity status of Class I types and of defined haplotypes spanning the MHC region of rhesus macaques. The work delineated in Aim #3 continues an existing process that has addressed the needs of the CNPRC for genetic characterization and management of animals in the SPF program and the rhesus colony at large. It expands into the implementation of state-of-the-art technology for transitioning into the routine use of SNP technology as the genotyping method of choice. The combined expertise in virology and genetics at CNPRC and of our collaborators provide the ideal intellectual resources for the establishment of an SPF breeding colony that is genetically characterized and MHC-defined.